@article{SisLab1858,
          volume = {7534},
          author = {Thi Hau Nguyen and Jean-Philippe Doyon and St{\'e}phanie Pointet and Anne-Muriel Arigon Chifolleau and Vincent Ranwez and Vincent Berry},
       booktitle = {Algorithms in Bioinformatics},
           title = {Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference},
         journal = {Lecture Notes in Computer Science},
             doi = {10.1007/978-3-642-33122-0\_10},
           pages = {123--134},
            year = {2012},
             url = {https://eprints.uet.vnu.edu.vn/eprints/id/eprint/1858/},
        abstract = {We propose a reconciliation heuristic accounting for gene duplications, losses and horizontal transfers that specifically takes into account the uncertainties in the gene tree. Rearrangements are tried for gene tree edges that are weakly supported, and are accepted whenever they improve the reconciliation cost. We prove useful properties on the dynamic programming matrix used to compute reconciliations, which allows to speed-up the tree space exploration when rearrangements are generated by Nearest Neighbor Interchanges (NNI) edit operations. Experimental results on simulated and real data confirm that running times are greatly reduced when considering the above-mentioned optimization in comparison to the na{\"i}ve rearrangement procedure. Results also show that gene trees modified by such NNI rearrangements are closer to the correct (simulated) trees and lead to more correct event predictions on average. The program is available at http://www.atgc-montpellier.fr/ Mowgli/}
}